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1 Dr. Charles Ofria Computer Science and Engineering 2140 Engineering Building, Michigan State University East Lansing, MI 48824 [email protected] - http://www.cse.msu.edu/~ofria/ EDUCATION California Institute of Technology 1994-1999 Ph.D. Computation and Neural Systems May 1999 Advisor: Dr. Christoph C. Adami Thesis: "Evolution of Genetic Codes" State University of New York at Stony Brook 1991-1994 B.S. Computer Science, Pure Math, and Applied Math May 1994 RESEARCH EXPERIENCE Professor July 2013-Present Associate Professor July 2008-June 2013 Assistant Professor July 2002-June 2008 Computer Science and Engineering Ecology, Evolutionary Biology, and Behavior Michigan State University, East Lansing MI Research Assistant Professor Oct. 1999-June 2002 Research Associate Aug. 1999-Sept 1999 Advisor: Dr. Richard E. Lenski Center for Microbial Ecology and Center for Biological Modeling Michigan State University, East Lansing MI Postdoctoral Research Associate June 1999-July 1999 Graduate Research Assistant Aug. 1994-May 1999 Advisor: Dr. Christoph C. Adami Computation and Neural Systems California Institute of Technology, Pasadena CA TEACHING EXPERIENCE Courses at Michigan State University: Instructor: CSE 450 - Translation of Programming Languages Spring 2004, 2005, 2006, 2007 Fall 2013, 2014, 2015 Instructor: CSE 491 - Digital Evolution and Biocomplexity Spring 2005 Instructor: CSE 830 - Design and Theory of Algorithms Spring 2000,2003,2008,2015 Fall 2002,2005,2009,2011 Co-Instructor: CSE 845 Multidisciplinary Methods for the Study of Evolution Spring 2014 Instructor: CSE 891 - Digital Evolution and Biocomplexity Fall 2003, Spring 2007, 2009 Co-Instructor: CSE 891 Multidisciplinary Methods for the Study of Evolution Spring 2011, 2012 Co-Instructor: BCH 960 - Topics in Biological Modeling Spring 2001 Co-Instructor: QB 827 Problems in Quantitative Biology Fall 2009 Instructor: ZOL 890 - Special Topics in Digital Evolution: The Avida Platform Spring 2002

2 Guest Lecturer for courses at MSU: ZOL 890: Evolutionary Biology for non-Biologists Fall 2010, 2011 CSE 848: Evolutionary Computation Spring 2003, 2005, 2007, Fall 2008, 2010 MTH 370: Mathematical Biology Spring 2007 MMG 433: Microbial Genomics Spring 2003 CSE Graduate Seminary Series Fall 2003, 2004, 2006 AWARDS AND HONORS Withrow Teaching Award Mar. 2010 18th place in nation - 2009 Google U.S. Puzzle Championship June 2009 16th place in nation - 2008 Google U.S. Puzzle Championship June 2008 NSF CAREER Award April 2007 Front page headline story on research, Lansing State Journal (Sunday, Nov 26) Nov 2006 Withrow Distinguished Scholar Award Mar. 2006 MSU Teacher/Scholar Award Feb. 2006 Finalist, Microsoft New Faculty Fellowship May 2005 Cover Story, February 2005 Discover Magazine Feb. 2005 Interview on WKAR Morning Edition on NPR Feb. 2005 Best Paper Award, Artificial Life IV Conference July 2004 Runner-Up, Clauser Award for best Ph.D. thesis, California Institute of Technology May 1999 National Science Foundation Fellowship Sept. 1994-Aug 1998 Gift of Computer Equipment from Microsoft Corporation Aug. 1997 First Horatio G. Burchard Award for Creativity and Quick Thinking May 1994 (From the Computer Science and Applied Math departments at SUNY Stony Brook) GRANTS Active LENs: Learning Evolution and the Nature of Science using Evolution Dec 2014-August 2019 in Action from the National Science Foundation. With R. Pennock, L. Mead, J. Smith, and R. Lenski. $1,844,969 BEACON: An NSF Center for the Study of Evolution in Action from the August 2010-July 2020 National Science Foundation. With E. Goodman, R. Lenski, R. Pennock and K. Holekamp. $47,500,000 Predictive Biology: Adaptability Robustness and the Fundamental Laws of Sept 2009-Sept 2010 Biology from DARPA. With R. Lenski. $730,000 ORCHID: Harnessing Digital Evolution to Design High-Assurance June 2008-June 2012 Adaptive Systems from the National Science Foundation. With B. Cheng, P. McKinley, and X. Tan. $600,000 CRI:IAD A Testbed for Evolving Adaptive and Cooperative Behavior May 2008-April 2009 Among Autonomous Systems from the National Science Foundation. With P. McKinley, X. Tan, R Pennock, and B. Cheng. $188,110 SGER Applying Digital Evolution to Behavioral Models from the National Sept 2007-Sept 2008 Science Foundation. With B. Cheng, P. McKinley, and R. Lenski. $100,000 CAREER: Digital Evolution and Biocomplexity From Biological Theory April 2007-March 2013 to Computational Applications. from the National Science Foundation. $400,000

3 Planning grant: Center for Software-Intensive Ultra-Large-Scale Systems Jan 2007-Dec 2007 from the National Science Foundation. With B. Cheng, S. Biswas, P. McKinley, and L. Dillon. $10,000 FunBio: Mathematical and Biological Studies of Fitness Landscapes from Jan 2006-Dec 2009 DARPA. With R. Lenski and P. Bates. $2,700,000 Emerging Intelligence: Contingency, Convergence and Constraints in the Jan 2006-Dec 2008 Evolution of Intelligent Behavior from the John Templeton Foundation. With R. Pennock and R. Lenski. 168,000 (approx. $300,000) EMT: Reimagining Evolutionary Computation, from the National Science July 2005-July 2009 Foundation CCF-0523449. With R. Lenski. $300,000 Avida-ED: Technology for Teaching Evolution and the Nature of Science Feb 2004-Feb 2008 using Digital Organisms, from the National Science Foundation DUE-0341484. With R. Pennock, D. Ebert-May, and R. Lenski. $255,836 ITR: Evaluating Phylogeny Reconstruction Algorithms with Digital Organisms. Sept 2002-Aug 2007 from the National Science Foundation EIA-0219229. With E. Torng and T. Schmidt. $324,722 PROFESSIONAL ACTIVITIES Reviewer for professional journals: Artificial Life; Communications of the ACM; IEEE Proceedings of Artificial Intelligence; Journal of Theoretical Biology; Nature; Physica D; PLoS (Public Library of Science) journals: PLoS Biology, PLoS Computational Biology, and PLoS ONE; Proceedings of the National Academy of Sciences; Proceedings of the Royal Socity of London; South African Journal of Science; The American Naturalist; Program committee for journal special issues: Artificial Life: Evolution of Complexity (2007), Artificial Life: Research with Avida (2004). Program committees for professional conferences: European Conference on Artificial Life (ECAL) 2005, 2009, 2011, 2015 Genetic and Evolutionary Computation Conference (GECCO) 2003-Present International Conference on Artificial Life (ALIFE). 1998-Present At Michigan State University: Search Committee Teaching Specialist in Computer Science Aug 2015- Present Awards Committee Department of Computer Science Aug 2015- Present Retreat Planning Committee Ecology, Evolutionary Biology & Behavior Program Aug 2015- Present Search Committee John P. Koza Chair in Genetic Programming Oct 2014-July 2015 Computational Mathematics, Science, & Engineering (CMSE) Steering Committee Sept 2014-Present Early Career Awards Committee Sept 2014 Theme Leader: Computational Evolution, BEACON Center July 2014-Present Search Committee BEACON Information Technologist Feb 2014 Search Committee BEACON Distinguished Postdoctoral Fellowship (Annual) Dec 2013-Present Biomedical Engineering Graduate Studies Committee Aug 2013-May 2014 Promotion & Tenure Committee Computer Science & Engineering July 2013-Present Advisory Board CAFFE Program October 2011 Search Committee Diversity Director, BEACON Center Sept 2010-Feb 2011 Executive Committee, BEACON Center for the Study of Evolution in Action Sept 2010-Present Deputy Director, BEACON Center for the Study of Evolution in Action Aug 2010-Present Search Committee Koenig Endowed Chair of Electrical Engineering July 2010-Mar 2011

4 Research Experience for Teachers Mentor June 2010-Sept 2011 Search Committee Director of the Institute for Cyber-Enabled Research (ICER) June 2010-May 2012 Representative of MSU, Congressional NSF Day April 2010 Quatitative Biology Initiative Advisory Committee Aug 2009-May 2012 Chair, Steering Committee Institute for Cyber-Enabled Research (ICER) May 2009-Present University-wide Cyber-Enabled Discovery Visioning Committee Mar 2008-Oct 2008 Ad Hoc Committee for the redesign of the Computer Science web site June 2007-June 2008 Ad Hoc Committee for the redesign of the College of Engineering web site May 2007-June 2008 Ad Hoc Committee for Engineering and Health Initiative Feb 2007-Jan. 2008 Mentor, Graduate Fellowship Proposal Preparation Group Aug 2006-Nov 2011 Department of Computer Science Advisory Committee June 2006-May 2012 Department of Computer Science Curriculum Committee Aug 2005-May 2006 Quantitative Biology Fellowship Committee May 2005-May 2010 Department of Computer Science Faculty Search Committee Oct 2004-May 2006; Oct 2007-May 2008 Co-Chair, Quantitative Biology and Modeling Seminar Series Sept 2004-May 2008 Advisory Board Quantitative Biology and Modeling May 2003-Nov 2007 Faculty Advisor ACM Club, MSU Chapter Aug. 2003-May 2011 Computer Science Graduate Studies and Research Committee Aug 2002-May 2005 and Nov. 2009-Present Faculty Advisor MSU Medical Yoga Club Aug 2001-Aug 2011 Search Committee - Computational Biochemisty/Biophysics Nov 2002-May 2003 Co-Chair, Biological Modeling Seminar Series Sept. 2000-May 2001 Founding member, Center for Biological Modeling July 2000 Other activities: Academic Editor, Journal of Artificial Life July 2015-Present Academic Editor, PeerJ Jan 2015-Present External Reviewer, Hampshire College School of Cognitive Science self evaluation Mar 2014 Chair, Thirteenth International Conference on Artificial Life (held July 2012) Oct 2010-Jan 2013 Panelist, National Science Foundation CAREER Awards Oct 2009 Invited Participant, DARPA workshops on the Fundamental Laws of Biology Mar 2007, Aug 2008 Invited Participant, NSF workshop on Emerging Models and Technologies July 2008 Proposal Reviewer for the National Science Foundation Feb 2007 Invited Participant, Formation of NSF Program on Advancing Theory in Biology Sept. 2006 Invited Participant, DARPA workshop on Microbial Cooperation Aug 2006 Invited Participant, Seaver Workshops on Evolution of Computer Viruses Sept 2005, July 2006 Invited Participant, DARPA workshop on Fitness Landscapes Feb 2006 Invited Participant, Microsoft Faculty Summit July 2005 Invited Participant, Santa Fe Workshop on the Road to Software Evolvability June 2005 Invited Participant, Santa Fe Workshop on Evolution of Robustness April 2002 Algorithm Consultant, Personal Spider Inc., Pasadena CA Aug. 2000-May 2001 Security Consultant, SmartTrac Computer Systems, East Setauket NY May 1994-July 1994 Algorithm Consultant, Tadmus Worldwide, Bohemia NY Mar. 1994-May 1994

5 CURRENT GRADUATE STUDENTS Alex Lalejini Spring 2020 (expected) Dual-PhD student in Computer Science and EEBB Topic: To be decided. Emily Dolson Spring 2018 (expected) Dual-PhD student in Computer Science and EEBB Topic: Interaction of Evolutionary and Ecological Dynamics Anselmo Pontes Spring 2018 (expected) Dual-PhD student in Computer Science and EEBB Topic: The Evolution of Gene Regulatory Networks Anya Johnson Spring 2017 (expected) Dual-PhD student in Computer Science and EEBB Topic: The Evolution of Cooperation Rosangela Canino-Koning Dual-PhD student in Computer Science and Ecology, Evo. Biology & Behavior Spring 2016 (expected) Topic: The Interplay of Evolvability and Modularity FORMER GRADUATE STUDENTS Anuraag Pakanati PhD student in Computer Science April 2015 Topic: The Evolutionary Acquisition of Information Current: Software Engineer, Xoran Technologies Luis Zaman Dual-PhD student in Computer Science and EEBB June 2014 Topic: The Evolution of Parasitic and Mutualistic Behaviors Current: NSF Postdoc, University of Washington Bess Walker Dual-PhD in Computer Science and Ecology, Evolutionary Biology & Behavior December 2012 Topic: The Effects of Ecosystems on the Evolution of Complexity Current: Software Engineer, Aptify David Bryson Dual-PhD in Computer Science and Ecology, Evolutionary Biology & Behavior August 2012 Topic: The Importance of Contingency in the Evolution of Complex Functions Current: Software Engineer, Apple Inc. Matthew Rupp Dual-PhD in Computer Science and Ecology, Evolutionary Biology & Behavior April 2011 Topic: On the Evolution of Mutation Bias in Digital Organisms (co-advised with Prof. Eric Torng) Current: Postdoc, Michigan State University Heather Goldsby February 2011 Dual-PhD in Computer Science and Ecology, Evolutionary Biology & Behavior Topic: The Evolution of Division of Labor Current: Postdoc, University of Washington

6 Jeff Clune PhD in Computer Science April 2010 Topic: The Evolutionary Benefits of Generative Encodings (co-advised with Prof. Robert Pennock) Current: Assistant Professor, University of Wyoming Sherri Goings Dual-PhD in Computer Science and Ecology, Evolutionary Biology & Behavior April 2010 Topic: Natural Niching: Applying Ecological Principles to Evolutionary Computation Current: Assistant Professor, Carleton College Arthur Covert Dual-PhD in Computer Science and Ecology, Evolutionary Biology & Behavior December 2009 Topic: The Effects of Detrimental Mutations on Evolution Current: Postdoc, UT Austin Laura Grabowski PhD in Computer Science May 2009 Topic: The Early Evolution of Intelligence in Navigation Current: Assistant Professor, UT Pan American Gabriel Yedid Dual-PhD in Zoology and Ecology, Evolutionary Biology & Behavior April 2007 Topic: Evolution in Digital Ecologies (co-advised with Prof. Richard Lenski) Current: Assistant Professor, Nanjing Agricultural University, China Dusan Misevic Dual-PhD in Zoology and Ecology, Evolutionary Biology & Behavior April 2006 Topic: The Evolution of Sex (co-advised with Prof. Richard Lenski) Current: Postdoc, Institute National de la sant et de la recherche medical, Paris Wei Huang PhD in Computer Science December 2005 Topic: Measuring Biological Complexity Current: Business Analyst, Ipsen Dehua Hang PhD in Computer Science December 2005 Topic: Comparison of Phylogenetic Tree Reconstruction Algorithms (co-advised with Prof. Eric Torng) Current: AVP, Catastrophe Modeling at Allied World Reinsurance Elizabeth Ostrowski Dual PhD in Zoology and Ecology, Evolutionary Biology & Behavior May 2005 Topic: Long term evolution with digital organisms (co-advised with Prof. Richard Lenski) Current: Assistant Professor, University of Houston Michelle Vogel MS in Computer Science May 2013 Topic: Deep-branch phylogeny reconstruction Current: Software Engineer at Microsoft

7 Jason Stredwick MS in Computer Science December 2005 Topic: Evolution of Wire-Frame Organisms Current: Software Engineer at uTest (spun off from Google) Jinghua Zhang MS in Computer Science August 2001 Topic: Morphological Evolution in a 2D world Current: Associate Professor, Winston-Salem State University James Vanderhyde MS in Computer Science May 2001 Topic: Reconstructing phylogenetic trees (co-advised with Prof. Eric Torng) Current: Assistant Professor, Benedictine College POSTDOCTORAL RESEARCHERS Joshua Nahum Oct 2013-Present BEACON Distinguished Postdoctoral Fellow Aaron Wagner BEACON Center for the Study of Evolution in Action August 2010-March 2014 Current: Senior research scientist, Metron Corporation Jeffrey Barrick Microbiology and Molecular Genetics September 2006-December 2010 (co-sponsored with Richard Lenski) Current: Assistant Professor, UT Austin Christopher Strelioff August 2007-August 2010 Microbiology and Molecular Genetics (co-sponsored with Richard Lenski) Current: Postdoc, UC Davis Wesley Elsberry Lyman Briggs School January 2007-August 2009 (co-sponsored with Robert Pennock) Current: Scientific Programmer at the Fish and Wildlife Research Institute UNDERGRADUATE RESEARCHERS 34 undergraduate students have performed research as part of my research group: Mikaela Lias (Summer 2015-present), Riley Annis (Fall 2014-present), Erin OHara (Summer 2014-Spring2015), Rodny Perez (Summer 2014), Demetrius Moncrease (Fall 2013-Spring 2014), Grayson Wright (Fall 2011-Spring 2012), Jacob Walker (Summer 2011-Spring 2012), David Rogers (Spring 2011-present), James Bosko (Spring 2011-Spring 2012), Tasneem Pierce (Fall 2010-Summer 2011), Mairin Chesney (Fall 2010- present), Michelle Vogel (Summer 2010-Summer 2011), Owen Pierce (Spring 2010-Summer 2011), Suhas Devangam (Fall 2009-present), Nick Donohue (Summer 2009-Summer 2010), Meryl Mabin (Spring-Summer 2009), Isaac Fine (Summer 2008-Summer 2011), Andrew Melfi (Summer 2008-Fall 2008), Eric Muller (Fall 2007-Spring 2010), Chris Barott (Summer 2007), Caitlin Grabowski (Summers 2007-2008), Michael Vo (Fall 2006-Spring 2009), Andrew Kreling (Fall 2006-Spring 2007), James Pita (Fall 2005-Spring 2007), Randee Bierlein (Fall 2006), Katherine Simonds (Summer 2006-Fall 2006), Steen Wichmann (Summer 2006-Fall 2006), Jason Rapai (Fall 2005-Spring 2006), Thomas Levoy (Fall

8 2004-Spring 2006), Art Covert (Spring 2004-Fall 2004), Matt Rupp (Spring 2003-Spring 2004), Sherri Goings (Spring 2003-Fall 2003), George Hagstrom (Summers 2003 and 2004), Anastasha Kamps (Summer 2002), Larry Wisne (Fall 2002-Spring 2003), and Matthew Norconk (Fall 1999-Spring 2001) ACTIVE SOFTWARE PROJECTS Evoke Next generation digital evolution software 2014-Present https://github.com/mercere99/Evoke Empirical - Tools for developing web-based scientific software 2014-Present https://github.com/mercere99/Empirical TubeCode A virtual assembly language designed for teaching principles of compilers. 2014-Present https://github.com/mercere99/TubeCode EvoPuzzler Evolved web-based puzzles (http://www.puzzleengine.com) 2006-Present The Avida-ED Evolution Education Project (http://avida-ed.msu.edu/) 2003-Present The Avida Digital Evolution Research Platform 1993-Present https://github.com/devosoft/avida PEER-REVIEWED PUBLICATIONS Total Citations: 3953 H-Index: 25 i10-Index: 49 (From Google Scholar as of Oct 8th, 2015) 81. Ostrowski EA, Ofria C, Lenski RE (2015) Genetically integrated traits and rugged adaptive landscapes in digital organisms, BMC Evolutionary Biology, 15(1):83. 80. Zaman L, Meyer JR, Devengam S, Bryson DM, Lenski RE, and Ofria C. (2014) Coevolution Drives the Emergence of Complex Traits and Promotes Evolvability. PLoS Biology, 12.12: e1002023. 79. Biswas R, Ofria C, Bryson DM, and Wagner AP (2014). Causes vs Benefits in the Evolution of Prey Grouping. ALife 14: The Fourteenth Conference on the Synthesis and Simulation of Living Systems, pp. 641-648. 78. Goldsby HJ, Knoester DB, Kerr B, and Ofria C (2014) The Effect of Conflicting Pressures on the Evolution of Division of Labor. PLoS ONE, 9(8), e102713. 77. Johnson AE, Goldsby HJ, Goings S, and Ofria C. (2014) The evolution of kin inclusivity levels. Proceedings of the 2014 conference on Genetic and Evolutionary Computation. 76. Bryson DM, Wagner AP, and Ofria C (2014) There and back again: gene processing hardware for the evolution and robotic deployment of robust navigation strategies. Proceedings of the 2014 conference on Genetic and Evolutionary Computation. 75. Goldsby HJ, Knoester DB, Ofria C, and Kerr B (2014) The Evolutionary Origin of Somatic Cells under the Dirty Work Hypothesis. PLoS Biology, 12(5), e1001858. 74. Bryson DM and Ofria C (2013) Understanding Evolutionary Potential in Virtual CPU Instruction Set Architectures. PLoS ONE, 8(12), e83242.

9 73. Covert AW, Lenski RE, Wilke CO, and Ofria C (2013) Experiments on the role of deleterious mutations as stepping stones in adaptive evolution. Proceedings of the National Academy of Sciences, 110(34), E3171-E3178. 72. Taghizadeh M, Micinski K, Biswas S, Ofria C, and Torng E (2013) Distributed Cooperative Caching in Social Wireless Networks, IEEE Transactions on Mobile Computing, 12(6):1037-1053. 71. Grabowski LA, Bryson DM, Dyer FC, Pennock RT, and Ofria C (2013) A Case Study of the De Novo Evolution of a Complex Odometric Behavior in Digital Organisms, PLoS ONE. 70. Fortuna MA, Zaman L, Wagner AP, and Ofria C (2013) Evolving Digital Ecological Networks, PLoS Computational Biology. 69. Chandler CH, Ofria C, and Dworkin I (2013) Runaway Sexual Selection Leads to Good Genes, Evolution. 68. Goldsby H, Dornhaus A, Kerr B, and Ofria C (2012) Task Switching Costs Promote the Evolution of Division of Labor and Shifts in Individuality, Proc. Natl. Acad. Sci. USA, 109(34):13686-13691. 67. Clune J, Pennock RT, Ofria C, and Lenski RE (2012) Ontogeny Tends to Recapitulate Phylogeny in Digital Organisms, The American Naturalist, 180:E54-E63. 66. Goings S, Goldsby HJ, Cheng BHC, and Ofria C (2012) An Ecology-based Evolutionary Algorithm to Evolve Solutions to Complex Problems, Proceedings of the 13th International Conference for Artificial Life, East Lansing, MI. 65. Bryson DM, and Ofria C (2012) Digital Evolution Demonstrates Surprising Robustness to Poor Design Decisions, Proceedings of the 13th International Conference for Artificial Life, East Lansing, MI. 64. Goldsby H, Serra N, Dyer F, Kerr B, and Ofria C (2012) The Evolution of Temporal Polyethism, Proceedings of the 13th International Conference for Artificial Life, East Lansing, MI. 63. Zaman L, Ofria C, and Lenski RE (2012) Finger-painting Fitness Landscapes: An Interactive Tool for Exploring Complex Evolutionary Dynamics, Proceedings of the 13th International Conference for Artificial Life, East Lansing, MI. 62. Walker B and Ofria C (2012) Evolutionary Potential is Maximized at Intermediate Diversity Levels, Proceedings of the 13th International Conference for Artificial Life, East Lansing, MI. 61. Yedid G, Stredwick J, Nanlohy K, and Ofria C (2012) A Comparison of the Effects of Random and Selective Mass Extinctions on Erosion of Evolutionary History in Communities of Digital Organisms. PLoS ONE. 60. Grabowski LM, Bryson DM, Dyer FC, Pennock RT, and Ofria C (2011) Clever Creatures: Case Studies of Evolved Digital Organisms. Proceedings of the Proceedings of the 2011 European Conference on Artificial Life.

10 59. Connelly BD, Zaman L, Ofria C, and McKinley PK (2011) Modeling the Evolutionary Dynamics of Plasmids in Spatial Populations. Proceedings of the 2011 Genetic and Evolutionary Computation Conference. 58. Zaman L, Devangam S, and Ofria C (2011). Rapid Host-Parasite Co-Evolution Drives the Production and Maintenance of Diversity in Digital Organisms. Proceedings of the 2011 Genetic and Evolutionary Computation Conference. 57. Clune J, Stanley KO, Pennock RT, and Ofria C (2011). On the Performance of Indirect Encoding across the continuum of regularity. IEEE Transactions on Evolutionary Computation, 15:346-367. (73 Citations) 56. Clune J, Goldsby HJ, Ofria C, and Pennock RT (2011). Selective Pressures for Accurate Altruism Targeting: Empirical Support for Difficult-to-Test Aspects of Inclusive Fitness Theory, Proceedings of the Royal Society of London, 278(1706):666-674. 55. Strelioff CC, Ofria C, and Lenski RE (2010). Evolutionary Dynamics, epistatic interactions, and Biological Information. Journal of Theoretical Biology, 266(4):584-594. 54. Connelly BD, Zaman L, Ofria C, and McKinley PK (2010). Social Structure and the Maintenance of Biodiversity, The Proceedings of the 12th International Conference on Artificial Life, Odense, Denmark. Pages 461-468. 53. Grabowski LM, Bryson DM, Dyer F, Pennock RT, Ofria C (2010). Early Evolution of Memory Usage in Digital Organisms, The Proceedings of the 12th International Conference on Artificial Life, Odense, Denmark. Pages 224-231. 52. Clune J, Beckmann BE, McKinley PK, and Ofria C (2010). Investigating Whether HyperNEAT Produces Modular Neural Networks. The Proceedings of the 2010 Genetic and Evolutionary Computation Conference. Pages 634-642. (35 Citations) 51. Goldsby HJ, Knoester DB, and Ofria C (2010). Evolution of Division of Labor in Genetically Homogenous Groups. The Proceedings of the 2010 Genetic and Evolutionary Computation Conference. 50. Misevic D, Ofria C, and Lenski RE (2010). Experiments with Digital Organisms on the Origin and Maintenance of Sex in Changing Environments. Journal of Heredity. 101(supp 1):S46-54. doi:10.1093/jhered/esq017. 49. Clune J, Beckmann BE, Pennock RT, and Ofria C (2009). HybrID: A Hybridization of Indirect and Direct Encodings for Evolutionary Computation. Proceedings of the European Conference on Artificial Life (ECAL), 2009. Budapest, Hungary. 48. Goldsby H, Knoester DB, Clune J, McKinley PK, and Ofria C (2009). The Evolution of Division of Labor. Proceedings of the European Conference on Artificial Life (ECAL), 2009. Budapest, Hungary. 47. Clune J, Pennock R, and Ofria C (2009). The Sensitivity of HyperNEAT to Different Geometric Representations of a Problem. Proceedings of the 2009 Genetic and Evolutionary Computation Conference. (40 Citations)

11 46. Goldsby H, Goings S, Clune J, and Ofria C (2009). Problem Decomposition Using Indirect Reciprocity in Evolved Populations. Proceedings of the 2009 Genetic and Evolutionary Computation Conference, pages 105-112. 45. Clune J, Beckmann B, Ofria C, and Pennock R (2009). Evolving coordinated quadruped gaits using the HyperNEAT generative encoding. Proceedings of the IEEE Congress on Evolutionary Computations, Special Session on Evolutionary Robotics. (117 Citations) 44. Goings S and Ofria C (2009). Ecological Approaches to Diversity Maintenance in Evolutionary Algorithms. Proceedings of the IEEE Symposium on Artificial Life, pages 124-130. 43. Beckmann B, Grabowski L, McKinley P, and Ofria C (2009). Applying Digital Evolution to the Design of Self-Adaptive Software. Proceedings of the IEEE Symposium on Artificial Life. 42. Elsberry W, Grabowski L, Ofria C, and Pennock R (2009). Cockroaches, Drunkards, and Climbers: Evolving Simple Movement Strategies Using Digital Organisms. Proceedings of the IEEE Symposium on Artificial Life. 41. Yedid G, Ofria C, and Lenski RE (2009). Selective Press Extinctions, but Not Random Pulse Extinctions, Cause Delayed Ecological Recovery in Communities of Digital Organisms, The American Naturalist. 173(4):E139-E154. 40. Clune J, Misevic D, Ofria C, Lenski RE, Elena SF, and Sanjuan R (2008). Natural Selection Fails to Optimize Mutation Rates for Long-Term Adaptation on Rugged Fitness Landscapes, PLoS Computational Biology, 4(9): e1000187. doi:10.1371/journal.pcbi.1000187 (65 Citations) 39. Yedid G, Ofria C, and Lenski RE (2008). Historical and Contingent Factors Affect Re-Evolution of a Complex Feature Lost During Mass Extinction in Communities of Digital Organisms, Journal of Evolutionary Biology, 21(5):1335-1357. 38. Ofria C, Huang W and Torng E. (2008). On the Gradual Evolution of Complexity and the Sudden Emergence of Complex Features. Artificial Life, 14(3) 255-263. doi:10.1162/artl.2008.14.3.14302 36. Grabowski LM, Elsberry WR, Pennock RT, and Ofria C. (2008) On the Evolution of Motility and Intelligent Tactic Response, Proceedings of the ACM Genetic and Evolutionary Computation Conference (GECCO-2008), Atlanta GA, July 2008, Pages 209-216. http://doi.acm.org/10.1145/1389095.1389129 35. Knoester DB, McKinley PK, and Ofria C. (2008) Cooperative Network Construction Using Digital Germlines, Proceedings of the ACM Genetic and Evolutionary Computation Conference (GECCO- 2008), Atlanta GA, July 2008, Pages 217-224. 34. Beckmann B, McKinley PK, and Ofria C. (2008) Selection for Group-Level Efficiency Leads to Self- Regulation of Population Size, Proceedings of the ACM Genetic and Evolutionary Computation Conference (GECCO-2008), Atlanta GA, July 2008, Pages 185-192. 33. Clune J, Ofria C, and Pennock RT (2008) How a generative encoding fares as problem-regularity decreases. Proceedings of the 10th International Conference on Parallel Problem Solving From Nature. 358-367.

12 32. Goldsby HJ, Cheng BHC, McKinley PK, Knoester DB, and Ofria C. (2008) Digital Evolution of Behavioral Models for Autonomic Systems, Proceedings of the 5th IEEE International Conference on Autonomic Computing, Chicago IL, June 2008. Pages 86-96 (Best paper award). 31. McKinley PK, Cheng BHC, Ofria C, Knoester DB, Beckmann B, and Goldsby HJ. (2008) Harnessing Digital Evolution, IEEE Computer, 41(1):54-63. 30. Clune J, Ofria C, and Pennock RT. (2007) Investigating the Emergence of Phenotypic Plasticity in Evolving Digital Organisms, Lecture Notes in Computer Science (Proceedings of the 2007 European Conference on Artificial Life), 4648:74-83. 29. Beckmann B, McKinley PK, and Ofria C. (2007b) Evolution of an Adaptive Sleep Response in Digital Organisms, Lecture Notes in Computer Science (Proceedings of the 2007 European Conference on Artificial Life), 4648:233-242. 28. Knoester DB, McKinley PK, Beckmann B, and Ofria C. (2007b) Directed Evolution of Communication and Cooperation in Digital Organisms, Lecture Notes in Computer Science (Proceedings of the 2007 European Conference on Artificial Life), 4648:384-394. 27. Beckmann BE, McKinley PK, Knoester DB, and Ofria C. (2007a) Evolution of Cooperative Information Gathering in Self-Replicating Digital Organisms. Proceedings of the First IEEE International Conference on Self-Adaptive and Self-Organizing Systems (SASO), Boston, Massachusetts, July 2007. Pages 65-76. 26. Knoester DB, McKinley PK, and Ofria C. (2007a) Using Group Selection to Evolve Leadership in Populations of Self-Replicating Digital Organisms, Proceedings of the 2007 Genetic and Evolutionary Computation Conference, London, England, July 2007. Pages 293-300. 25. Hang D, Torng E, Ofria C, and Schmidt TM. (2007) The Effect of Natural Selection on the Performance of Maximum Parsimony. BMC Evolutionary Biology, 7:94. 24. McKinley PK, Cheng BHC, and Ofria C. (2007) Applying Digital Evolution to the Design of Self- Adaptive ULS Systems (position paper), in Proceedings of the Workshop Software Engineering for Adaptive and Self-Managing Systems, with ICSE 2007, Minneapolis, Minnesota, May 2007. 23. Goldsby HJ, Knoester DB, Cheng BHC, McKinley PK, and Ofria C. (2007) Digitally Evolving Models for Dynamically Adaptive Systems, in Proceedings of the Workshop Software Engineering for Adaptive and Self-Managing Systems, with ICSE 2007, Minneapolis, Minnesota, May 2007. 22. Elena SF, Wilke CO, Ofria C, and Lenski RE. (2007) Effects of population size and mutation rate on the evolution of mutational robustness. Evolution 61(3):666-674. 21. Ostrowski E, Ofria C, and Lenski RE (2007). Ecological specialization and adaptive decay in digital organisms, The American Naturalist 169:E1-E20. 20. Lenski RE, Barrick JE, Ofria C (2006). Balancing Robustness and Evolvability, PLoS Biology 4(12):e428. (145 Citations)

13 19. Rupp M, Torng E, and Ofria C (2006). The evolution of novel body types under differing selective pressures in digital organisms, Proceedings of the Tenth International Conference on Artificial Life (p268-274), Bloomington IN. 18. Misevic D, Ofria C, and Lenski RE (2006). Sexual reproduction reshapes the genetic architecture of digital organisms, Proceedings of the Royal Society of London 273:457-464. (99 Citations) 17. Chow S, Wilke CO, Ofria C, Lenski RE, and Adami C (2004). Adaptive Radiation from Resource Competition in Digital Organisms, Science 305:84-86. (117 Citations) 16. Ofria C and Wilke CO (2004). Avida: A Software Platform for Research in Computational Evolutionary Biology, Journal of Artificial Life, 10:191-229. (254 Citations) 15. Hagstrom GI, Hang DH, Ofria C, and Torng E (2004). Using Avida to Test the Effects of Natural Selection on Phylogenetic Reconstruction Methods, Journal of Artificial Life, 10:157-166. 14. Huang W, Ofria C, and Torng E (2004). Measuring Biological Complexity in Digital Organisms, Proceedings of the Ninth International Conference on Artificial Life (p315-321), Boston MA, Sept 12-15. 13. Goings S, Clune J, Ofria C, and Pennock R (2004). Kin Selection: The Rise and Fall of Kin- Cheaters, Proceedings of the Ninth International Conference on Artificial Life (p303-308), Boston MA, Sept 12-15. 12. Misevic D, Lenski RE, and Ofria C (2004). Sexual reproduction and Muller's ratchet in digital organisms, Proceedings of the Ninth International Conference on Artificial Life (p340-345), Boston MA, Sept 12-15. 11. de Visser JAGM, Hermisson J, Wagner GP, Ancel Meyers L, Bagheri-Chaichian H, Blanchard JL, Chao L, Cheverud JM, Elena SF, Fontana W, Gibson G, Hansen TF, Krakauer D, Lewontin RC, Ofria C, Rice SH, von Dassow G, Wagner A, and Whitlock MC (2003). Evolution and Detection of Genetic Robustness, Evolution, 57:1959-1972. (436 Citations) 10. Lenski RE, Ofria C, Pennock RT, and Adami C (2003). The Evolutionary Origin of Complex Features, Nature, 423:139-144. (527 Citations) 9. Ofria C, Adami C, and Collier TC (2003). Selective Pressures on Genomes in Molecular Evolution, J. Theor. Biology 222:477-483. (46 Citations) 8. Hang D, Ofria C, Schmidt TS, Torng E (2003). The Effect of Natural Selection on Phylogeny Reconstruction Algorithms, Proceedings of the 2003 Genetic and Evolutionary Computation Conference, pp.13-24. 7. Ofria C, Adami C, and Collier TC (2002). Design of Evolvable Computer Languages, IEEE Transactions in Evolutionary Computation, 17:528-532. (48 Citations) 6. Cooper T and Ofria C (2002). Evolution of stable ecosystems in populations of digital organisms, Proceedings of the Eighth International Conference on Artificial Life, pp. 227-232. Dec 9-13, Sydney NSW Australlia, Russell K. Standish, Mark A. Bedau and Hussein A. Abbass (eds.)

14 5. Wilke CO, Wang J, Ofria C, Adami C, and Lenski RE (2001). Evolution of Digital Organisms at High Mutation Rate Leads To Survival of the Flattest, Nature, 412:331-333. (464 Citations) 4. Adami C, Ofria C and Collier TC (2000). Evolution of Biological Complexity, Proc. Natl. Acad. Sci. USA 97:4463-4468. (428 Citations) 3. Lenski RE, Ofria C, Collier TC, and Adami C (1999). Genome complexity, robustness and genetic interactions in digital organisms, Nature 400, 661-664. (256 Citations) 2. Ofria C, Adami C, Collier TC, and Hsu GK (1999). The evolution of differentiated expression patterns in digital organisms, Lect. Notes Artif. Intell. 1674:129-138. 1. Ofria C and Adami C (1999). Evolution of Genetic Organization in Digital Organisms. Proc. of DIMACS workshop Evolution as Computation, Jan 11-12 Princeton, NJ, Landweber L and Winfree E, eds (Springer) pp. 167-175. EXTENDED ABSTRACTS 5. Grabowski LM, Bryson DM, Dyer FC, Pennock RT, and Ofria C (2012). An Analysis of the De Novo Evolution of a Complex Odometric Behavior, Proceedings of the 13th International Conference for Artificial Life, East Lansing, MI. 4. Canino-Koning R and Ofria C (2012). The Evolution of Modularity Under Changing Environments in Digital Organisms, Proceedings of the 13th International Conference for Artificial Life, East Lansing, MI. 3. Misevic D, Ofria C, Lenski RE (2011). Digital Sex: Causes and Consequences, Proceedings of the European Conference on Artificial Life, pp.532-533. 2. Clune J, Ofria C, and Pennock RT (2008). How Generative Encodings Fare on Less Regular Problems, Proceedings of the ACM Genetic and Evolutionary Computation Conference (GECCO- 2008), Atlanta GA, July 2008, Pages 867-868. 1. Beckmann B, Grabowski L, McKinley PK, and Ofria C. (2008) Autonomic Software Development Methodology Based on Darwinian Evolution, Proceedings of the 5th IEEE International Conference on Autonomic Computing, Chicago IL, June 2008. Page 203. BOOKS 1. Adami C, Bryson DM, Ofria C, and Pennock RT, editors (2012). Artificial Life 13: Proceedings of the 13th International Conference on the Simulation and Synthesis of Living Systems, East Lansing, MI. MIT Press, Cambridge, MA. OTHER PUBLICATIONS

15 3. Ofria C, Bryson DM, and Wilke CO (2009). Avida: A Software Platform for Research in Computational Evolutionary Biology. Published in Artificial Life Models in Software by Adamatzky A. and Komosinski M. (Eds.), Springer Verlag, London, UK, second edition, July 2009 2. Ofria C and Wilke CO (2005). Avida: Evolution Experiments with self-replicating computer programs, in Artificial Life Models in Software by Adamatzky A and Komosinski M (eds.), Springer Verlag, London, p 3-35. 1. Ofria C, Brown CT, and Adami C (1998). The Avida Technical Manual, Published in Introduction to Artificial Life by Christoph Adami, Telos Springer Verlag, New York, pages 297-350.

16 INVITED PRESENTATIONS June 4, 2015 Active LENS Workshop, East Lansing, MI March 13, 2015 Research Lecture, University of Louisville, Louisville, KY March 12, 2015 Public Lecture, University of Louisville, Louisville, KY August 3, 2014 Artificial Life 14 Summer School, New York, NY. April 18, 2014 Metron Corporation, Washington D.C. April 16, 2014 University of Texas at Austin, Austin TX June 23, 2013 SSE Evolution Education Symposium: Evolution Out of Bounds May 9, 2013 Keynote for Genetic Programming in Theory and Practice (GPTP) March 19, 2013 American Physical Society March 16, 2012 MSU Community Club July 29, 2011 Northrup Grumman Corporation July 15, 2011 Genetic and Evolutionary Computation Conference February 18-23, 2011 University of Washington (3 talks) October 8, 2009 Google Tech Talk March 12, 2009 North Carolina A&T State University September 7, 2007 Keynote talk for Molecular Biology Retreat, Princeton University February 2, 2007 Public Lecture at The Los Angeles Natural History Museum November 29, 2006 University of Texas at Austin (2 talks) November 27, 2006 Rice University October 31, 2006 Massachusetts Institute of Technology, Artificial Intelligence Lab October 30, 2006 Brandeis University, Department of Computer Science September 28, 2006 The National Science Foundation, Workshop on Advancing Theory in Biology August 26, 2006 DARPA Workshop on Microbial Cooperation March 2, 2006 The Ohio State University February 10, 2006 University of Arkansas at Little Rock February 4, 2006 DARPA Workshop on Fitness Landscapes (Berkeley, CA) November 14, 2005 Workshop on Self-Organization in Evolution (Mathematical Biosciences Inst.) June 23, 2005 Workshop on the Road to Software Evolvability (Santa Fe Institute) May 6, 2005 Microsoft Research April 14, 2005 MIT Biological Engineering February 24, 2005 The American Museum of Natural History October 8, 2004 University of Idaho September, 2004 Medical College of Ohio May 21, 2004 LinkEcol Conference (European Science Foundation) November 13, 2003 University of Akron September 3, 2003 Yale University November 15, 2002 Butler University April 8, 2002 Stanford University

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